Variant report

Variant	rs2531820
Chromosome Location	chr6:28456719-28456720
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28446745..28449657-chr6:28455146..28458037,3	MCF-7	breast:
2	chr6:27858756..27861228-chr6:28455818..28458096,2	K562	blood:
3	chr6:28372326..28375748-chr6:28455628..28458983,4	K562	blood:
4	chr6:28456446..28459153-chr6:28555326..28557057,2	MCF-7	breast:
5	chr6:28187359..28189911-chr6:28455377..28457870,2	K562	blood:
6	chr6:28451721..28454293-chr6:28455250..28457902,2	MCF-7	breast:
7	chr6:28455757..28458631-chr6:28484303..28486741,3	K562	blood:
8	chr6:28456451..28458356-chr6:28686774..28688606,2	K562	blood:
9	chr6:28364266..28370257-chr6:28453674..28463075,14	K562	blood:
10	chr6:28455752..28457337-chr6:28581196..28584117,2	K562	blood:
11	chr6:28188045..28189911-chr6:28456370..28458760,2	K562	blood:
12	chr6:28192543..28195348-chr6:28455724..28457783,2	K562	blood:
13	chr6:28455084..28458229-chr6:28499553..28502958,3	K562	blood:
14	chr6:28364227..28369783-chr6:28455559..28460332,7	K562	blood:
15	chr6:27858485..27861228-chr6:28455818..28458807,3	K562	blood:
16	chr6:28446299..28448037-chr6:28455509..28457029,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000158691	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000232040	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000137185	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1015811	0.94[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1016069	0.85[EUR][1000 genomes]
rs2531817	0.85[ASN][1000 genomes]
rs2859351	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462666	chr6:28417222-28574415	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv601210	chr6:28417222-28574415	Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1020689	chr6:28449137-28635171	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28451800-28456800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:28455200-28457600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:28456400-28456800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr6:28456400-28456800	Enhancers	HepG2	liver
5	chr6:28456400-28456800	Flanking Active TSS	K562	blood
6	chr6:28456400-28457000	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr6:28456400-28457800	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr6:28456400-28458000	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr6:28456400-28458200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:28456400-28458200	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr6:28456400-28458400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr6:28456400-28459400	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr6:28456400-28460200	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr6:28456600-28456800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:28456600-28456800	Bivalent Enhancer	Adipose Nuclei	Adipose
16	chr6:28456600-28456800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr6:28456600-28456800	Bivalent Enhancer	Fetal Thymus	thymus
18	chr6:28456600-28457000	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:28456600-28457000	Flanking Active TSS	Fetal Lung	lung
20	chr6:28456600-28457000	Enhancers	Placenta	Placenta
21	chr6:28456600-28457000	Bivalent Enhancer	Thymus	Thymus
22	chr6:28456600-28457200	Flanking Active TSS	Placenta Amnion	Placenta Amnion
23	chr6:28456600-28457400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
24	chr6:28456600-28457600	Active TSS	Brain Angular Gyrus	brain
25	chr6:28456600-28458200	Active TSS	H1 Cell Line	embryonic stem cell
26	chr6:28456600-28458200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr6:28456600-28458400	Active TSS	H9 Cell Line	embryonic stem cell
28	chr6:28456600-28458400	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr6:28456600-28458400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr6:28456600-28458400	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr6:28456600-28458600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr6:28456600-28458600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr6:28456600-28458600	Active TSS	Ovary	ovary
34	chr6:28456600-28458800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr6:28456600-28458800	Active TSS	A549	lung
36	chr6:28456600-28458800	Active TSS	GM12878-XiMat	blood

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